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Transcriptomic Analysis of Organotypic Porcine Retina Cultures.

Overview

Authors: Siavash Khosravi1, Grazia Giorgio1, Federica Staurenghi1, Tanja Schoenberger1, Peter Gross1, Margit Ried1, Julia Frankenhauser1, Sebastian Eder1, Elke Markert1, Remko A Bakker1, Sepideh Babaei1, Nina Zippel1
ORCID iDs: Tanja Schoenberger, Sepideh Babaei
  1. Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riss, Germany; (S.K.); (G.G.); (F.S.); (T.S.); (J.F.); (S.E.); (E.M.); (R.A.B.); (S.B.)
Institutions: Boehringer Ingelheim (Germany) (Germany)
Journal: International journal of molecular sciences, volume 27, issue 9, article 3901
Dates: received 8 February 2026; accepted 25 April 2026; published online 28 April 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.3390/ijms27093901 · PMID 42123486 · PMCID PMC13163581 · OpenAlex W7156888181
Open access: gold, a free copy (OpenAlex)
Status: data only
Categories: genetics / omics (modality), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Preprocessing, Connectivity
Keywords: porcine retina, ex vivo culture, transcriptomic, RNA sequencing
MeSH: Gene Expression Profiling*, Retina*, Transcriptome*, Animals, Organ Culture Techniques, Swine (* major topic)
Topic: Retinal Development and Disorders (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Citations: cited by 1 paper (Europe PMC); 32 references in the paper

Abstract

Porcine organotypic retinal explant cultures are widely used to study retinal neurodegeneration under controlled conditions, but the biological processes that occur in the retinal explant over time due to preparation-induced injury and culture are not well understood. Here, we generated a time-resolved transcriptomic reference for porcine neural retinal explants, which were maintained ex vivo for 10 days. Global expression profiles are strongly separated by culture time, with Day 0 clearly distinct from cultured samples and Day 7 and Day 10 showing the highest similarity, indicating a transition toward a later stabilized state. Across the time course, 3187 genes were differentially expressed relative to Day 0, with the largest shifts occurring at an early stage of culture (Day 1–Day 3). Pathway-level analyses revealed coordinated remodeling involving inflammatory signaling and metabolic/bioenergetic changes, including reduced mitochondrial and oxidative phosphorylation-related programs at later time points. Here, we provide a time-resolved transcriptomics reference dataset for cultured porcine retinal explants. These data can build a foundation to interpret data generated in this model, differentiate changes inherent to the explant culture from treatment-specific effects and select appropriate experimental windows for mechanistic studies of retinal degeneration.

Reproduced under the paper's license (CC BY), from the paper cited above.

Code

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Data

Datasets cited

Data Availability Statement

The porcine RNA sequencing data generated in this study are deposited in GEO repository (accession number GSE318246 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE318246)).

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 12 authors, 4 keywords, 6 MeSH terms, 32 references.

Cite

This paper

Khosravi, S., Giorgio, G., Staurenghi, F., Schoenberger, T., Gross, P., Ried, M., Frankenhauser, J., Eder, S., Markert, E., Bakker, R. A., Babaei, S., & Zippel, N. (2026). Transcriptomic Analysis of Organotypic Porcine Retina Cultures. International journal of molecular sciences, 27(9), 3901. https://doi.org/10.3390/ijms27093901

BibTeX

@article{khosravi2026transcriptomic,
author = {Khosravi, Siavash and Giorgio, Grazia and Staurenghi, Federica and Schoenberger, Tanja and Gross, Peter and Ried, Margit and Frankenhauser, Julia and Eder, Sebastian and Markert, Elke and Bakker, Remko A and Babaei, Sepideh and Zippel, Nina},
title = {{Transcriptomic Analysis of Organotypic Porcine Retina Cultures}},
journal = {International journal of molecular sciences},
year = {2026},
month = apr,
volume = {27},
number = {9},
pages = {3901},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
issn = {1422-0067},
doi = {10.3390/ijms27093901},
url = {https://doi.org/10.3390/ijms27093901},
pmid = {42123486},
pmcid = {PMC13163581}
}

RIS

TY - JOUR
AU - Khosravi, Siavash
AU - Giorgio, Grazia
AU - Staurenghi, Federica
AU - Schoenberger, Tanja
AU - Gross, Peter
AU - Ried, Margit
AU - Frankenhauser, Julia
AU - Eder, Sebastian
AU - Markert, Elke
AU - Bakker, Remko A
AU - Babaei, Sepideh
AU - Zippel, Nina
TI - Transcriptomic Analysis of Organotypic Porcine Retina Cultures
T2 - International journal of molecular sciences
J2 - Int J Mol Sci
PY - 2026
DA - 2026/04/28
VL - 27
IS - 9
SP - 3901
SN - 1422-0067
PB - Multidisciplinary Digital Publishing Institute (MDPI)
DO - 10.3390/ijms27093901
UR - https://doi.org/10.3390/ijms27093901
LA - en
ER -

CSL-JSON

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